mkin/tests/testthat/FOCUS_2006_D.csf, branch v1.0.4Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.0.42020-11-19T15:03:38ZUpdate tests, improve CAKE_export test2020-11-19T15:03:38ZJohannes Rankejranke@uni-bremen.de2020-11-19T15:03:38Zurn:sha1:300c0fccf327b9959db39c256bae0974908e59b2Skip vdiffr tests on travis as they are not robust2020-11-11T09:43:56ZJohannes Rankejranke@uni-bremen.de2020-11-11T09:43:56Zurn:sha1:0cbabc98850e436b1e0703c659cf8a00b52d7503
As can be seen in the miniscule change seen on R-devel in the reference
plot updated with this commit
Improve saem method, add summary2020-11-08T01:12:55ZJohannes Rankejranke@uni-bremen.de2020-11-08T01:12:55Zurn:sha1:279a1d83d7cbe39a953467762629eb1abb9addf4
Also make the endpoints function work for saem objects.
Create saem generic for fitting saemix models2020-11-07T11:54:58ZJohannes Rankejranke@uni-bremen.de2020-11-07T11:54:58Zurn:sha1:2e37905a7bf0d72751ee7326ef05a268989e49b2
The reasons for this decision were
- Creating an saemix generic in the saemix package caused problems with
roxygen, because functions like saemix.plot.xy were documented in
their help files as S3 methods, although explicitly exported with
@export
- Creating an saemix generic in this package is possible, but would
make it necessary to load samix with exclude = "saemix" in order to
avoid overwriting the generic when loading saemix.
- The return object of such an saemix generic in this package cannot
be an S3 class with class attribute c("saemix.mmkin", "SaemixObject")
similar to nlme.mmkin, as saemix returns an S4 class.
- Extending the S4 class SaemixObject using simple inheritance to
a class SaemixMmkinObject with additional slots did not work
as expected. When the initialize method was left untouched, it
prevented creation of an SaemixMmkinObject even if it was based
on an initialised SaemixObject, as the initialize method seems
to always be called by new(). This could potentially be circumvented
by a coerce method. If an alternative initialize method was
used, an SaemixMmkinObject could be created. However, the methods
written for SaemixObjects only worked in some instances, either
because they checked for the class, and not for class inheritance
(like compare.saemix), or because the initialize method was called
for some reason. Therefore, the idea of creating a derived S4 class
was abandoned.
- A side effect of this decision is that the introduction of the saem
generic opens the possibility to use the same generic also for other
backends like nlmixr with the SAEM algorithm.
Fast analytical solutions for saemix, update.mmkin2020-11-05T23:03:29ZJohannes Rankejranke@uni-bremen.de2020-11-05T23:03:29Zurn:sha1:b5b446b718b15ccaae5b197e147fc1358f0f564e
Also, use logit transformation for g and for solitary formation
fractions, addressing #10.
Revert to use starting values for random effects in nlme.mmkin2020-11-04T09:06:34ZJohannes Rankejranke@uni-bremen.de2020-11-04T09:06:34Zurn:sha1:f24a86c1f33e06c8114021c5c3956b5f7c400c18Add summary method for nlme.mmkin objects2020-10-27T14:36:46ZJohannes Rankejranke@uni-bremen.de2020-10-27T14:34:14Zurn:sha1:a5874ab7fce4616e80be69366ff0685332f47bf1
Improve and update docs
Fix issues for release2020-10-08T07:31:35ZJohannes Rankejranke@uni-bremen.de2020-10-08T07:31:35Zurn:sha1:bc3825ae2d12c18ea3d3caf17eb23c93fef180b8mkinfit: Ignore unused components of state.ini2020-07-17T14:27:46ZJohannes Rankejranke@uni-bremen.de2020-07-17T14:27:46Zurn:sha1:a7e209b553e2e99ffc9aa2b003f9b73b9ac4b985Improve handling of (partially) failing fits2020-07-15T10:30:39ZJohannes Rankejranke@uni-bremen.de2020-07-15T10:30:39Zurn:sha1:9f8e1eb33b586beb7e889212bdababa081b6ff67